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New developments in space radiation research at NASA: Annotating data using a novel radiation biology ontology

Like many interdisciplinary sciences, data producers and consumers in the field of radiation biology often use a wide variety of terminology to describe their experiments and data. Furthermore, space systems and technologies are rapidly evolving, and a shared understanding and common terminology for these is also lacking. The efficiency of research organizations can be enhanced by standardizing metadata through the use of knowledge resources like ontologies. Employing a sophisticated model such as a formal ontology to standardize metadata enables automated data acquisition processes and supports more complete, accurate meta-analysis through more efficient and complete data discovery and retrieval, particularly when using multiple data sources. Thus, we developed the Radiation Biology Ontology (RBO) in order to improved radiation biology metadata uniformity and transparency. We used open-source software (the Ontology Development Kit, Protégé and WebProtégé) and worked within the OBO Foundry framework, which includes a set of ontology development principles and practices for ontology consistency, uniformity, and accountability. The RBO has now been incorporated into two radiation research data repositories, NASA’s GeneLab omics database (https://genelab.nasa.gov), and the European Commission STORE database (https://www.storedb.org/). Continuous build integration tools allowed our international RBO collaboration to be more efficient and focus its efforts on semantic model design. Currently, the RBO contains over 300 annotated classes and individuals specific to the study of radiation on biological systems, as well as imports of many additional classes from other OBO Foundry ontologies that relate to and/or provide context for these RBO entities. We publish the RBO through the OBO Foundry, so that it is available for browsing, download, and querying through NCBI Bioportal web site and application programming interface. The NASA Ames Life Science Data Archive (ALSDA) is also in the process of adopting use of the RBO, taking NASA one step closer to a knowledge-based system for space biology data. It is our hope that the global communities of radiation research Investigators, data curators and data analysts can similarly leverage the RBO and will contribute to its further development.

radiation↗

Commentary 2 to Cox and Little: radiation-induced oncogenic transformation: the interplay between dose, dose protraction, and radiation quality

There is now a substantial body of evidence for end points such as oncogenic transformation in vitro, and carcinogenesis and life shortening in vivo, suggesting that dose protraction leads to an increase in effectiveness relative to a single, acute exposure--at least for radiations of medium linear energy transfer (LET) such as neutrons. Table I contains a summary of the pertinent data from studies in which the effect is seen. [table: see text] This phenomenon has come to be known as the "inverse dose rate effect," because it is in marked contrast to the situation at low LET, where protraction in delivery of a dose of radiation, either by fractionation or low dose rate, results in a decreased biological effect; additionally, at medium and high LET, for radiobiological end points such as clonogenic survival, the biological effectiveness is independent of protraction. The quantity and quality of the published reports on the "inverse dose rate effect" leaves little doubt that the effect is real, but the available evidence indicates that the magnitude of the effect is due to a complex interplay between dose, dose rate, and radiation quality. Here, we first summarize the available data on the inverse dose rate effect and suggest that it follows a consistent pattern in regard to dose, dose rate, and radiation quality; second, we describe a model that predicts these features; and, finally, we describe the significance of the effect for radiation protection.

Review, Tutorial↗

Report on the Radiation Effects Testing of the Infrared and Optical Transition Radiation Camera Systems

Presented in this report are the results tests performed at Argonne National Lab in collaboration with Los Alamos National Lab to assess the reliability of the critical 99 Mo production facility beam monitoring diagnostics. The main components of the beam monitoring systems are two cameras that will be exposed to radiation during accelerator operation. The purpose of this test is to assess the reliability of the cameras and related optical components when exposed to operational radiation levels. Both X-ray and neutron radiation could potentially damage camera electronics as well as the optical components such as lenses and windows. This report covers results of the testing of component reliability when exposed to X-ray radiation. With the information from this study we provide recommendations for implementing protective measures for the camera systems in order to minimize the occurrence of radiation-induced failure within a ten month production run cycle.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Differential Mobility Spectrometry-Mass Spectrometry (DMS-MS) in Radiation Biodosimetry: Rapid and High-Throughput Quantitation of Multiple Radiation Biomarkers in Nonhuman Primate Urine

High-throughput methods to assess radiation exposure are a priority due to concerns that include nuclear power accidents, the spread of nuclear weapon capability, and the risk of terrorist attacks. Metabolomics, the assessment of small molecules in an easily accessible sample, is the most recent method to be applied for the identification of biomarkers of the biological radiation response with a useful dose-response profile. Profiling for biomarker identification is frequently done using an LC-MS platform which has limited throughput due to the time-consuming nature of chromatography. We present here a chromatography-free simplified method for quantitative analysis of seven metabolites in urine with radiation dose-response using urine samples provided from the Pannkuk et al. (2015) study of long-term (7-day) radiation response in nonhuman primates (NHP). The stable isotope dilution (SID) analytical method consists of sample preparation by strong cation exchange-solid phase extraction (SCX-SPE) to remove interferences and concentrate the metabolites of interest, followed by differential mobility spectrometry (DMS) ion filtration to select the ion of interest and reduce chemical background, followed by mass spectrometry (overall SID-SPE-DMS-MS). Since no chromatography is used, calibration curves were prepared rapidly, in under 2 h (including SPE) for six simultaneously analyzed radiation biomarkers. The seventh, creatinine, was measured separately after 2500× dilution. Creatinine plays a dual role, measuring kidney glomerular filtration rate (GFR), and indicating kidney damage at high doses. The current quantitative method using SID-SPE-DMS-MS provides throughput which is 7.5 to 30 times higher than that of LC-MS and provides a path to pre-clinical radiation dose estimation. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Radiation Therapy for Primary Cutaneous Anaplastic Large Cell Lymphoma: An International Lymphoma Radiation Oncology Group Multi-institutional Experience

Purpose: To collect response rates of primary cutaneous anaplastic large cell lymphoma, a rare cutaneous T-cell lymphoma, to radiation therapy (RT), and to determine potential prognostic factors predictive of outcome. Methods and Materials: The study was a retrospective analysis of patients with primary cutaneous anaplastic large cell lymphoma who received RT as primary therapy or after surgical excision. Data collected include initial stage of disease, RT modality (electron/photon), total dose, fractionation, response to treatment, and local recurrence. Radiation therapy was delivered at 8 participating International Lymphoma Radiation Oncology Group institutions worldwide. Results: Fifty-six patients met the eligibility criteria, and 63 tumors were treated: head and neck (27%), trunk (14%), upper extremities (27%), and lower extremities (32%). Median tumor size was 2.25 cm (range, 0.6-12 cm). T classification included T1, 40 patients (71%); T2, 12 patients (21%); and T3, 4 patients (7%). The median radiation dose was 35 Gy (range, 6-45 Gy). Complete clinical response (CCR) was achieved in 60 of 63 tumors (95%) and partial response in 3 tumors (5%). After CCR, 1 tumor recurred locally (1.7%) after 36 Gy and 7 months after RT. This was the only patient to die of disease. Conclusions: Primary cutaneous anaplastic large cell lymphoma is a rare, indolent cutaneous lymphoma with a low death rate. This analysis, which was restricted to patients selected for treatment with radiation, indicates that achieving CCR was independent of radiation dose. Because there were too few failures (<2%) for statistical analysis on dose response, 30 Gy seems to be adequate for local control, and even lower doses may suffice.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

The Importance of Radiation Dose to the Atherosclerotic Plaque in the Left Anterior Descending Coronary Artery for Radiation-Induced Cardiac Toxicity of Breast Cancer Patients?

Radiation-induced acute coronary events (ACEs) may occur as a treatment-related late adverse effect of breast cancer (BC) radiation. However, the underlying mechanisms behind this radiation-induced cardiac disease remain to be determined. The objective of this study was to test the hypothesis that radiation dose to calcified atherosclerotic plaques in the left anterior descending coronary artery (LAD) is a better predictor for ACEs than radiation dose to the whole heart or left ventricle in patients with BC treated with radiation therapy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Investigation of Arctic Cloud Properties and Surface Radiation Based on MOSAiC Shipborne Observations

The Arctic is rapidly changing due to changes of the Earth system. This study investigates cloud fraction, phase partition, cloud type, and their relationships with surface radiation based on yearlong shipborne observations in the Arctic regions. The Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) campaign provided lidar and radar observations of cloud microphysical properties and surface shortwave (SW) and longwave (LW) radiation. Cloud and radiative properties were examined at daily and monthly resolutions in four seasons. Low clouds were found to be most prevalent throughout the year, followed by deep clouds. The ice phase is the dominant phase except for summer (June–August). Liquid and mixed phases show more significant monthly and annual mean radiative effects in SW and LW than the ice phase. The clouds show net warming effects due to LW heating in most months, while the SW cooling effects of clouds become more dominant for July and August. The cloud and radiation observations from MOSAiC were used to evaluate simulations of the atmospheric component of the Energy Exascale Earth System Model version 2. The simulations show large overestimations of the liquid and mixed phases in the Arctic regions from February to September. The simulations also underestimate the percentages of low clouds and overestimate the percentages of deep clouds throughout the year. Altogether, this work provides a unique analysis of cloud and radiation properties based on high-resolution shipborne observations, which can be used to assist future model evaluation and development.

58 GEOSCIENCES↗

Measurement of the radiative decay rate and energy of the metastable (2s{sup 2}2p{sub 1/2}{sup 5}3s{sub 1/2}){sub (J=0)} level in Fe xvii

Measurements at the Livermore electron beam ion trap have been performed in order to infer the energy and the radiative lifetime of the (1s{sup 2}2s{sup 2}2p{sub 1/2}{sup 5}3s{sub 1/2}){sub J=0} level in the Fe xvii spectrum. This is the longest-lived level in the neonlike iron ion, and its radiative decay produces the Fe xvii line at 1153 Å, feeding the population of the (1s{sup 2}2s{sup 2}2p{sub 3/2}{sup 5}3s{sub 1/2}){sub J=1} upper level of one of the most prominent lines in the Fe xvii L-shell X-ray spectrum, commonly dubbed 3G. In the presence of a strong (⩾ few kG) magnetic field, the (1s{sup 2}2s{sup 2}2p{sub 1/2}{sup 5}3s{sub 1/2}){sub J=0} level has a finite probability to decay directly to the (1s{sup 2}2s{sup 2}2p{sup 6}){sub J=0} neonlike ground level via the emission of an L-shell X-ray. Our measurements allow us to observe this X-ray line in the Fe xvii L-shell spectrum and from it to infer the radiative rate for the magnetic dipole decay of the (1s{sup 2}2s{sup 2}2p{sub 1/2}{sup 5}3s{sub 1/2}){sub J=0} level to the (1s{sup 2}2s{sup 2}2p{sub 3/2}{sup 5}3s{sub 1/2}){sub J=1}. Our result of (1.45±0.15)×10{sup 4} s{sup −1} is in agreement with predictions. We have also measured the wavelength of the associated X-ray line to be 16.804 ± 0.002 Å, which means that the line is displaced 1.20 ± 0.05 eV from the neighboring (2s{sup 2}2p{sub 1/2}{sup 5}3s{sub 1/2}){sub J=1}→(2s{sup 2}2p{sup 6}){sub J=0} transition, commonly labeled 3F. From our measurement, we infer 5950570 ± 710 cm{sup −1} for the energy of the (1s{sup 2}2s{sup 2}2p{sub 1/2}{sup 5}3s{sub 1/2}){sub J=0} level.

79 ASTRONOMY AND ASTROPHYSICS↗

Dose, LET, time and strain dependence of radiation-induced 53BP1 foci in 15 mouse strains ex vivo and associations to in vivo radiation susceptibility

We present a comparative analysis on the repair of radiation-induced DNA damage ex vivo in 15 strains of mice, including 5 inbred reference strains and 10 collaborative-cross strains, of both sexes. Non-immortalized primary skin fibroblasts derived from 76 mice were subjected to both low- and high-LET radiation (0.1, 1 and 4 Gy of X rays; 1.1 and 3 particles/100μm2 of 350 MeV/n 40Ar and 600 MeV/n 56Fe). Automated image quantification of 53BP1 radiation-induced foci (RIF) during the first 4-48 h post-irradiation was performed as a function of dose and LET. Similarly to what we had previously reported for immortalized human cell lines [1], we observed a saturation of RIF number with dose at 4h post-irradiation, with more RIF/Gy for lower LET (X rays and 40Ar) compared to 56Fe. However at later time points (24h and above), the trend was inverted with more RIF/Gy for higher LET. Our data suggest that multiple DSBs cluster into RIF: as the linear density of DSBs increases with LET, so does the probability of having more DSBs per RIF, which makes it more difficult for cells to fully resolve high-LET-induced RIF, explaining the hypersensitivity to high-LET radiation despite a low number of RIF. Taking into account the amount of clustering at a given dose and LET, but also the kinetics of DNA damage repair, we introduced a novel mathematical formalism to evaluate the number of remaining RIF over time. We showed that the newly introduced kinetic metrics can be used as surrogate biomarkers for in vivo radiation toxicity, with potential applications in radiotherapy and human space exploration. In particular, we observed an association between the repairable fraction of RIF measured in vitro and survival levels of immune cells collected from irradiated mice. Moreover, the speed of DNA damage repair correlated with spontaneous cancer incidence data collected from the Mouse Tumor Biology database, suggesting a relationship between the efficiency of DSB repair after irradiation and cancer risk. In addition to the efficacy of repair and persistent RIF levels, even the amount of spontaneous foci without irradiation was shown to be strain dependent, indicating that these phenotypes are at least partially driven by genetics, and supporting their potential as indicators of individual radiation sensitivity. [1] Neumaier, T., et al., PNAS, 2012 (8) 109:443

Radiation, DNA damage, repair kinetics↗

INCREASING THE TRANSPARENCY AND REPRODUCIBILITY OF SPACE RADIATION SCIENCE: THE RADIATION BIOLOGY ONTOLOGY

Among the primary objectives of the Open/Open-Source Science paradigm are making scientific investigation data transparent and results reproducible [1], objectives shared by the FAIR principles [2]. To accomplish this, the conceptual framework that includes all the investigation objects needs to be accurately captured and communicated to all data consumers. A large part of this requires using metadata standards to annotate data collected. These standards should be readily accessible, informed by scientific community consensus and sufficiently specific to encompass all of the important aspects of the investigation. Starting in 2020 we have been co-leading an open consortium to develop a new metadata standard, the Radiation Biology Ontology (RBO), through the Open Biological and Biomedical Ontologies (OBO) Foundry [3]. We began by transforming many of the terms from the National Council on Radiation Protection and Measurement into concepts that can be formally related to existing OBO Foundry classes or attributes. We then identified and imported into the RBO existing OBO Foundry classes that have obvious relevance for radiation biomedicine (for example, concepts from the Environment Ontology that describe radiative processes, and concepts from the Gene Ontology dealing with molecular and cellular responses to radiation). Finally, we scrutinized datasets from investigations of radiation effects held in NASA GeneLab and LSDA repositories and added additional classes, instances, and attributes into the RBO that should be used to annotate these data. We developed the RBO using the open-source tools of GitHub and publish the RBO periodically through the NIH/NCBI BioPortal website, so systems worldwide can leverage the knowledge it contains [4]. This initial phase of concept modeling has yielded an RBO that at present has more than 300 declared concepts, with more than 3500 additional concepts imported from other OBO Foundry ontologies. While this first phase has focused on concepts for annotating samples, environments, exposures, and measurements, the next phase will center on supporting annotation of results and findings, such as concept models of molecular, cellular and tissue effects. The value of the RBO will be determined in part by our ability to engage the community in its development, and we have established a Radiobiology Informatics Consortium with unrestricted membership as the owner of the RBO in order to encourage investigators, system owners and other to join in this effort. Anyone can report issues or request new concept modeling or other features directly on GitHub. By using the BioPortal application programming interface, systems can pose dynamic queries to the latest version of the RBO for information on individual classes or entire hierarchies; this design eliminates the need for systems to be updated in order to use newer versions of the RBO. We hope to contribute to the advancement of open radiobiological science through the continued, open development of the RBO, that will provide more precise, machine-interpretable descriptions of investigations, as well as support data meta-analysis through machine learning or other artificial intelligence methods.

knowledge↗

Efficient smoothed particle radiation hydrodynamics I: Thermal radiative transfer

This work presents efficient solution techniques for radiative transfer in the smoothed particle hydrodynamics discretization. Two choices that impact efficiency are how the material and radiation energy are coupled, which determines the number of iterations needed to converge the emission source, and how the radiation diffusion equation is solved, which must be done in each iteration. The coupled material and radiation energy equations are solved using an inexact Newton iteration scheme based on nonlinear elimination, which reduces the number of Newton iterations needed to converge within each time step. During each Newton iteration, the radiation diffusion equation is solved using Krylov iterative methods with a multigrid preconditioner, which abstracts and optimizes much of the communication when running in parallel. The code is verified for an infinite medium problem, a one-dimensional Marshak wave, and a two and three-dimensional manufactured problem, and exhibits first-order convergence in time and second-order convergence in space. For these problems, the number of iterations needed to converge the inexact Newton scheme and the diffusion equation is independent of the number of spatial points and the number of processors.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Radiation burnthrough measurements to infer opacity at conditions close to the solar radiative zone–convective zone boundary

Recent measurements at the Sandia National Laboratory of the x-ray transmission of iron plasma have inferred opacities much higher than predicted by theory, which casts doubt on modeling of iron x-ray radiative opacity at conditions close to the solar convective zone-radiative zone boundary. An increased radiative opacity of the solar mixture, in particular iron, is a possible explanation for the disagreement in the position of the solar convection zone-radiative zone boundary as measured by helioseismology and predicted by modeling using the most recent photosphere analysis of the elemental composition. In this report we present data from radiation burnthrough experiments, which do not support a large increase in the opacity of iron at conditions close to the base of the solar convection zone and provide a constraint on the possible values of both the mean opacity and the opacity in the x-ray range of the Sandia experiments. The data agree with opacity values from current state-of-the-art opacity modeling using the CASSANDRA opacity code.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Dalitz plot analyses of J / ψ → π + π - π 0 , J / ψ → K + K - π 0 , and J / ψ → K s 0 K ± π ∓ produced via e + e - annihilation with initial-state radiation

Here, we study the processes e + e - → γ ISR J/ψ , where J/ψ → π + π - π 0 , J/ψ → K + K - π 0 , and J / ψ → K$0\atop{S}$ K ± π ∓ using a data sample of 519 fb -1 recorded with the BABAR detector operating at the SLAC PEP-II asymmetric-energy e + e - collider at center-of-mass energies at and near the Υ (nS) (n = 2 , 3 , 4) resonances. We measure the ratio of branching fractions R 1 = $B(J/ψ →K^+K^- π^0)\atop{B(J/ψ →π^+π^- π^0)}$ and R 2 = $B(J/ψ →K^0_SK^±π^∓)\atop{B(J/ψ →π^+π^- π^0)}$. We perform Dalitz plot analyses of the three J/ψ decay modes and measure fractions for resonances contributing to the decays. We also analyze the J/ψ → $π^+π^- π^0$ decay using the Veneziano model. We observe structures compatible with the presence of ρ (1450) in all three J/ψ decay modes and measure the relative branching fraction: R (p(1450)) = $Bp(1450)→K^+K^-)\atop{B(p(1450)→π^+π^-)}$ +0.307 ± 0.084 (stat) ± 0.082 (sys).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Terrestrial radiative cooling: Using the cold universe as a renewable and sustainable energy source

Photonic materials designed at wavelength scales have enabled a range of emerging energy technologies, from solid-state lighting to efficient photovoltaics that have transformed global energy landscapes. Daytime passive radiative cooling materials shed heat from the ground to the cold universe by taking advantage of the terrestrial thermal radiation that is as large as the renewable solar energy. Newly developed photonic materials permit subambient cooling under direct sunshine, and their applications are expanding rapidly enabled by scalable manufacturing. We review here the recent advancement of daytime subambient radiative cooling materials, which allow energy-efficient cooling and are paving the way toward technologies that harvest the coldness from the universe as a new renewable energy source.

Science & Technology - Other Topics↗